Have you wiggled the headphone jack to be sure it's not just a bad connection?
I had a similar problem a few days ago trying to record a rough track of a song idea. I have to plug the mic into this thing before I boot up or it won't see it at all, and when I tried the initial recording I had only one side. It should be stereo. Wiggled the jack a couple of times and it started recording stereo, as it should, it's a stereo mic.
Now I have to see if I have a decent sounding condenser mic, that one was tinny as all hell...too much treble, almost no bass...but it got the song idea down so I can work on it some more later on. That's what matters for what I was trying to do. For that I don't care what it sounds like, as long as I capture the idea before I forget it...it sucks that I don't have my multitrack unit any more. It worked great with a stage mic, Shure PE 35L, but the friend who gave it to me died last year (partial payment for a job I did) and his widow decided to take it back when she got mad at me. I wouldn't play the funeral song she wanted me to learn, he had made it abundantly clear he did NOT want a funeral...I promised him I would have no part of the funeral he told me he was sure she was going to do anyway, she did, got mad at me and now I don't have a good recording unit any more...ad she lied to me to get it...
OK sorry to stray so far off topic...it just gets to me sometimes, like when I try to record something and no longer have the equipment I worked for.
I had the same problem when I first started to use that multitrack unit. The line out plugs were dirty, and one of the sliders. Crummy sound, crackly, no stereo, I had to get out the contact cleaner and go through everything before it started working right. Drove me nuts...
I've had this problem several times, dirty connections causing both headphones and mics to get only one side. Wiggle it to clean up the connection or use some contact cleaner. I use Audacity, works great but a bad connection will do the same thing no matter what software you use.
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